The original Motorola Droid came with stock Android and was a huge success. Then Motorola decided to become a little too confident and try to mess with how Android looks. It didn't turn out very well for them because their skin was probably the most hated Android skin from a manufacturer out there. Its name didn't help either – Motoblur.
Since then they've tried to move more towards a more stock-looking skin with "Gingerblur" (community named), and now that they are on the verge of being acquired by Google, it seems they are getting even closer to using little else besides the stock Android version with the Ice Cream Sandwich update for the Motorola RAZR.
It's too bad they aren't going 100% stock Android, but we'll take whatever we can get for now. However, once Google buys Motorola, they will just be one and the same company, so it would make very little sense for Google to make one version of Android (the stock one), and then have Motorola add even more stuff on top of that.
So I really don't think Motorola will use anything else besides stock Android once they are acquired. Google will put the Motorola developers under the main Android team, and then they'd all work together on new Android features that all Android phones will have. The difference will be that Motorola will probably be the only one using pure Android.
Carriers might not be too happy about everyone using stock Android, which is far from that being the case right now, but manufacturers can always customize Android in many different ways, that users themselves can already do right now. So I'd like this to be the direction that both the manufacturers and Google, by giving them the right tools, take into the future.